
TechRxiv
A preprint server for health sciences.

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

Minimap2 is a fast sequence alignment program designed for aligning DNA or mRNA sequences against a reference database. It excels at handling long, noisy reads generated by PacBio or Oxford Nanopore sequencing technologies, as well as short reads from Illumina platforms. The tool uses minimizers to index the reference genome, enabling efficient identification of potential alignment locations. It supports various alignment modes, including genomic read mapping, splice-aware alignment for RNA-seq data, assembly-to-assembly alignment, and finding overlaps between long reads. Minimap2's speed and accuracy make it suitable for large-scale genomic analyses, assembly polishing, and comparative genomics, providing biologically meaningful alignments ready for downstream analyses.
Minimap2 is a fast sequence alignment program designed for aligning DNA or mRNA sequences against a reference database.
Explore all tools that specialize in read mapping. This domain focus ensures Minimap2 delivers optimized results for this specific requirement.
Aligns RNA sequences to a reference genome, identifying splice junctions.
Handles long, error-prone reads generated by PacBio and Nanopore sequencing.
Aligns two genome assemblies to identify structural differences.
Utilizes SIMD instructions for accelerated sequence alignment.
Indexes the reference genome using minimizers for efficient sequence lookup.
Produces alignment output in PAF format, suitable for downstream analyses and visualization.
Install a C compiler, GNU make, and zlib development files.
Clone the Minimap2 repository from GitHub: `git clone https://github.com/lh3/minimap2`
Navigate to the Minimap2 directory: `cd minimap2`
Compile the source code: `make`
Add the Minimap2 executable to your system's PATH for easy access.
Index the reference genome: `./minimap2 -d ref.mmi ref.fa`
Align reads to the reference: `./minimap2 -a ref.mmi reads.fq > alignment.sam`
All Set
Ready to go
Verified feedback from other users.
"Minimap2 is highly regarded for its speed and accuracy in sequence alignment, particularly for long reads and splice-aware alignment."
Post questions, share tips, and help other users.

A preprint server for health sciences.

Connect your AI agents to the web with real-time search, extraction, and web crawling through a single, secure API.

Book trusted help for home tasks.

A large conversational telephone speech corpus for speech recognition and speaker identification research.

STRING is a database of known and predicted protein-protein interactions.

A free and open-source software package for the analysis of brain imaging data sequences.

Complete statistical software for data science with powerful statistics, visualization, data manipulation, and automated reporting in one intuitive platform.